Helicobacter pylori are spiral, microaerophilic bacteria that persistently colonize the human stomach, and that are associated with diseases of the upper gastrointestinal tract. There is increasing evidence that H. pylori individuals are colonized by a cloud of clonal variants, analogous to the quasi-species of RNA viruses. The ability of H. pylori to diversify appears crucial to its in vivo persistence, with increasing evidence of ongoing diversification involving multiple loci. For example, variation involving cagA and cagY affect host tissue interactions. In addition to endogenous point mutations, the H. pylori genome contains extensive and non-randomly distributed repetitive DNA, and the organisms are naturally competent for uptake of DNA from other H. pylori strains; these provide important mechanisms for diversification; substantial evidence indicates that this occurs in vivo. The hypothesis of this proposal is that H. pylori uses genetic variation as a principal mechanism to adapt to (dynamic) host environments. We will study recombination between repetitive DNA (Aim 1) and natural transformation (Aim 2) to examine the characteristics of these diversification methods. These studies will be conducted in vitro using quantitative assays that explore the mechanisms involved, and using construction of relevant H. pylori mutants to test the specific hypotheses raised. We will use in silico, experimental, and mathematical approaches to characterize these mechanisms, and then use the information and approaches to study phenotypic variation and its selection in an animal model (Aim 3). We will continue to focus on the selection for H. pylori cell surface Lewis antigen variation in a Leb-transgenic mouse model. The existence of this experimental system will allow analysis of the genetic mechanisms leading to genotypic changes, producing altered phenotypes. The experimental results will enable development of deterministic models relating genotypic and phenotypic variation with selection. [unreadable] [unreadable]